[gmx-users] Compile Gromacs with OpenCL for MacBook Pro with AMD Radeon Pro 560 GPU
Michael Williams
michael.r.c.williams at gmail.com
Tue Feb 19 22:59:01 CET 2019
Hi Szilárd, thank you for the suggestion. I modified the file "src/gromacs/gpu_utils/gpu_utils_ocl.cpp” and replaced both instances of “#ifdef __APPLE__” with “#if 0”. I then checked that the build and regression tests worked without enabling the GPU support. All of the tests passed. Then, in a new build folder, I added -DGMX_GPU=ON and -DGMX_USE_OPENCL=ON to the Cmake instructions (see below). I did this separately for the unmodified version of GROMACS 2018.5 as well as inside a separate copy where I’d made the above changes. When I ran “make check” for both the unmodified and modified versions, I got the same error as before (logs pasted below). However, it seems to happen at different parts of the test suite: the unmodified version passed the MdrunTests, then failed on one of the MdrunMpiTests. The modified version of GROMACS failed during MdrunTests and then passed the MdrunMpiTests.
During both runs of the tests I got a system popup asking if I wanted to allow the test executable that was running to accept incoming network connections. The window was only visible for a few seconds and I didn’t click either option (allow / deny) before the window went away again.
Thanks again for your help, and if you have any other ideas I’d be quite willing to try them out and let you know the results.
Mike
Build settings on MacBook Pro (OSX 10.14.3, Mojave) using system clang and OpenMP library (from LLVM 7.0.1) built in custom path (no other parts of LLVM 7.0.1 are installed in this path):
cmake .. -DCMAKE_INSTALL_PREFIX=/Users/michael/.local/apps/gromacs-2018.5-apple-clang-omp \
-DCMAKE_PREFIX_PATH=/Users/michael/.local \
-DCMAKE_C_COMPILER=/usr/bin/clang \
-DCMAKE_CXX_COMPILER=/usr/bin/clang++ \
-DCMAKE_C_FLAGS="-Wno-deprecated-declarations -Wno-unused-command-line-argument -Xpreprocessor -fopenmp -lomp -I/Users/michael/.local/include -L/Users/michael/.local/lib” \
-DCMAKE_CXX_FLAGS="-Wno-deprecated-declarations -Wno-unused-command-line-argument -Xpreprocessor -fopenmp -lomp -I/Users/michael/.local/include -L/Users/michael/.local/lib” \
-DGMX_FFT_LIBRARY=fftw3 \
-DGMX_GPU=ON \
-DGMX_USE_OPENCL=ON \
-DREGRESSIONTEST_PATH=/Users/michael/.local/source/regressiontests-2018.5
(Note: tabs added to make the above command easier to read)
***ERROR LOG WITH UNMODIFIED GPU_UTILS_OCL.CPP:
Can not increase nstlist because an NVE ensemble is used
Using 2 MPI threads
Using 1 OpenMP thread per tMPI thread
On host veronika.local 1 GPU auto-selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 2 ranks on this node:
PP:0,PP:0
NOTE: Your choice of number of MPI ranks and amount of resources results in using 1 OpenMP threads per rank, which is most likely inefficient. The optimum is usually between 2 and 6 threads per rank.
Compilation of source file /Users/michael/.local/source/gromacs-2018.5/src/gromacs/mdlib/nbnxn_ocl/nbnxn_ocl_kernels.cl failed!
-- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_ -DGMX_OCL_FASTGEN -DEL_CUTOFF -DEELNAME=_ElecCut -DLJ_COMB_GEOM -DVDWNAME=_VdwLJCombGeom -DCENTRAL=22 -DNBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER=8 -DNBNXN_GPU_CLUSTER_SIZE=8 -DNBNXN_GPU_JGROUP_SIZE=4 -DGMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY=4 -DNBNXN_MIN_RSQ=3.82e-07f -DIATYPE_SHMEM -cl-fast-relaxed-math -cl-denorms-are-zero -I/Users/michael/.local/source/gromacs-2018.5/src/gromacs/mdlib/nbnxn_ocl
--------------LOG START---------------
<program source>:80:10: fatal error: 'nbnxn_ocl_kernel_pruneonly.clh' file not found
#include "nbnxn_ocl_kernel_pruneonly.clh"
^
---------------LOG END----------------
-------------------------------------------------------
Program: mdrun-mpi-test, version 2018.5
Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 507)
Function: cl_program gmx::ocl::compileProgram(FILE *, const std::string &, const std::string &, cl_context, cl_device_id, ocl_vendor_id_t)
MPI rank: 1 (out of 2)
Internal error (bug):
Failed to compile NBNXN kernels for GPU #AMD Radeon Pro 560 Compute Engine
Could not build OpenCL program, error was CL_BUILD_PROGRAM_FAILURE
***ERROR LOG WITH MODIFIED GPU_UTILS_OCL.CPP:
Can not increase nstlist because an NVE ensemble is used
Using 1 MPI thread
Using 1 OpenMP thread
1 GPU auto-selected for this run.
Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:
PP:0
Compilation of source file /Users/michael/.local/source/gromacs-2018.5-mod/src/gromacs/mdlib/nbnxn_ocl/nbnxn_ocl_kernels.cl failed!
-- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_ -DGMX_OCL_FASTGEN -DEL_CUTOFF -DEELNAME=_ElecCut -DLJ_COMB_GEOM -DVDWNAME=_VdwLJCombGeom -DCENTRAL=22 -DNBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER=8 -DNBNXN_GPU_CLUSTER_SIZE=8 -DNBNXN_GPU_JGROUP_SIZE=4 -DGMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY=4 -DNBNXN_MIN_RSQ=3.82e-07f -DIATYPE_SHMEM -cl-fast-relaxed-math -cl-denorms-are-zero -I/Users/michael/.local/source/gromacs-2018.5-mod/src/gromacs/mdlib/nbnxn_ocl
--------------LOG START---------------
<program source>:80:10: fatal error: 'nbnxn_ocl_kernel_pruneonly.clh' file not found
#include "nbnxn_ocl_kernel_pruneonly.clh"
^
---------------LOG END----------------
-------------------------------------------------------
Program: mdrun-test, version 2018.5
Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 507)
Function: cl_program gmx::ocl::compileProgram(FILE *, const std::string &, const std::string &, cl_context, cl_device_id, ocl_vendor_id_t)
Internal error (bug):
Failed to compile NBNXN kernels for GPU #AMD Radeon Pro 560 Compute Engine
Could not build OpenCL program, error was CL_BUILD_PROGRAM_FAILURE
> On Feb 20, 2019, at 3:40 AM, Szilárd Páll <pall.szilard at gmail.com> wrote:
>
> We had some issues with the OS X OpenCL compilers being "special" and not
> accepting standard ways of passing include arguments.
>
> Can you try editing the
> src/gromacs/gpu_utils/gpu_utils_ocl.cpp
> file and replace "#ifdef __APPLE__" with "#if 0", compile the code and see
> if that works?
>
> --
> Szilárd
>
>
> On Tue, Feb 19, 2019 at 2:08 AM Michael Williams <
> michael.r.c.williams at gmail.com <mailto:michael.r.c.williams at gmail.com>> wrote:
>
>> Hi, I’ve been trying to build Gromacs 2018.3 on my MacBook Pro (in OSX
>> 10.14.3). I saw online (https://redmine.gromacs.org/issues/2369 <https://redmine.gromacs.org/issues/2369> <
>> https://redmine.gromacs.org/issues/2369 <https://redmine.gromacs.org/issues/2369>>) that Gromacs with GPU support
>> via OpenCL was found to work a similar computer, but I have not had any
>> luck. Is there a way to see what settings (compiler, CMake variables, etc)
>> were used for that build? Or if anyone has any suggestions, I’d be very
>> grateful. Thanks for your help,
>>
>> Mike
>>
>> The errors that I have been getting while running “make check” look like:
>>
>>
>> 1 GPU auto-selected for this run.
>> Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:
>> PP:0
>> Compilation of source file
>> /Users/michael/.local/source/gromacs-2018.3/src/gromacs/mdlib/nbnxn_ocl/
>> nbnxn_ocl_kernels.cl failed!
>> -- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_
>> -DGMX_OCL_FASTGEN -DEL_CUTOFF -DEELNAME=_ElecCut -DLJ_COMB_GEOM
>> -DVDWNAME=_VdwLJCombGeom -DCENTRAL=22
>> -DNBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER=8 -DNBNXN_GPU_CLUSTER_SIZE=8
>> -DNBNXN_GPU_JGROUP_SIZE=4 -DGMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY=4
>> -DNBNXN_MIN_RSQ=3.82e-07f -DIATYPE_SHMEM -cl-fast-relaxed-math
>> -cl-denorms-are-zero
>> -I/Users/michael/.local/source/gromacs-2018.3/src/gromacs/mdlib/nbnxn_ocl
>> --------------LOG START---------------
>> <program source>:80:10: fatal error: 'nbnxn_ocl_kernel_pruneonly.clh' file
>> not found
>> #include "nbnxn_ocl_kernel_pruneonly.clh"
>> ^
>> ---------------LOG END----------------
>>
>> -------------------------------------------------------
>> Program: mdrun-test, version 2018.3
>> Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 507)
>> Function: cl_program gmx::ocl::compileProgram(FILE *, const std::string
>> &, const std::string &, cl_context, cl_device_id, ocl_vendor_id_t)
>>
>> Internal error (bug):
>> Failed to compile NBNXN kernels for GPU #AMD Radeon Pro 560 Compute Engine
>> Could not build OpenCL program, error was CL_BUILD_PROGRAM_FAILURE
>> --
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